3LFY - JenaLib

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Title :   CTD OF TAROCYSTATIN IN COMPLEX WITH PAPAIN

Authors :   M. H. Chu, K. L. Liu, K. W. Yeh, Y. S. Cheng

Date :   19 Jan 10 (Deposition) - 21 Jul 10 (Release) - 21 Jul 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: C  (1x)

Keywords :   Cystatin, Tarocystatin, Cecpi, Papain, Phytocystatin, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. H. Chu, K. L. Liu, K. W. Yeh, Y. S. Cheng
Complex Structure Of Tarocystatin With Papain And Characterization Of Tarocystatin Proposed The Role Of C-Terminal Extension For Inhibitory Mechanism Of Group-2 Phytocystatins
To Be Published
PubMed: search

Molecule 1 - PAPAIN
	Chains	:	A, C
	EC Number	:	3.4.22.2
	Fragment	:	PAPAIN DOMAIN
	Organism Common	:	MAMON
	Organism Scientific	:	CARICA PAPAYA
	Organism Taxid	:	3649
	Other Details	:	PAPAIN WAS PURCHASED FROM SIGMA CO. FOR CO- CRYSTALLIZATION.
	Synonym	:	PAPAYA PROTEINASE I, PPI

		1	2
Asymmetric Unit	:	A	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 7)

No.	Name	Count	Type	Full Name
1	ASN	2	Mod. Amino Acid	ASPARAGINE
2	GLY	1	Mod. Amino Acid	GLYCINE
3	OCS	2	Mod. Amino Acid	CYSTEINESULFONIC ACID
4	SER	2	Mod. Amino Acid	SERINE

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	ASN	1	Mod. Amino Acid	ASPARAGINE
2	GLY	-1	Mod. Amino Acid	GLYCINE
3	OCS	1	Mod. Amino Acid	CYSTEINESULFONIC ACID
4	SER	1	Mod. Amino Acid	SERINE

Biological Unit 2 (4, 4)

No.	Name	Count	Type	Full Name
1	ASN	1	Mod. Amino Acid	ASPARAGINE
2	GLY	1	Mod. Amino Acid	GLYCINE
3	OCS	1	Mod. Amino Acid	CYSTEINESULFONIC ACID
4	SER	1	Mod. Amino Acid	SERINE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:177 , ASN A:214	BINDING SITE FOR RESIDUE SER A 213
2	AC2	SOFTWARE	GLN A:142 , TRP A:177 , SER A:213 , HOH A:296	BINDING SITE FOR RESIDUE ASN A 214
3	AC3	SOFTWARE	GLN C:19 , OCS C:25 , ASP C:158 , HIS C:159 , TRP C:177 , GLY C:214	BINDING SITE FOR RESIDUE SER C 213
4	AC4	SOFTWARE	GLY C:20 , TRP C:177 , SER C:213 , ASN C:215	BINDING SITE FOR RESIDUE GLY C 214
5	AC5	SOFTWARE	GLN C:142 , TRP C:177 , GLY C:214	BINDING SITE FOR RESIDUE ASN C 215

Asymmetric Unit

No.	Residues
1	A:22	-	A:63
2	A:56	-	A:95
3	A:153	-	A:200
4	C:22	-	C:63
5	C:56	-	C:95
6	C:153	-	C:200

Asymmetric Unit

No.	Residues
1	Gly A:151	-	Pro A:152
2	Gly C:151	-	Pro C:152

(no "SAP(SNP)/Variant" information available for 3LFY)

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOL_PROTEASE_CYS	PS00139	Eukaryotic thiol (cysteine) proteases cysteine active site.	PAPA1_CARPA	152-163	2	A:19-30 C:19-30
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	PAPA1_CARPA	290-300	2	A:157-167 C:157-167
3	THIOL_PROTEASE_ASN	PS00640	Eukaryotic thiol (cysteine) proteases asparagine active site.	PAPA1_CARPA	303-322	2	A:170-189 C:170-189

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOL_PROTEASE_CYS	PS00139	Eukaryotic thiol (cysteine) proteases cysteine active site.	PAPA1_CARPA	152-163	1	A:19-30 -
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	PAPA1_CARPA	290-300	1	A:157-167 -
3	THIOL_PROTEASE_ASN	PS00640	Eukaryotic thiol (cysteine) proteases asparagine active site.	PAPA1_CARPA	303-322	1	A:170-189 -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	THIOL_PROTEASE_CYS	PS00139	Eukaryotic thiol (cysteine) proteases cysteine active site.	PAPA1_CARPA	152-163	1	- C:19-30
2	THIOL_PROTEASE_HIS	PS00639	Eukaryotic thiol (cysteine) proteases histidine active site.	PAPA1_CARPA	290-300	1	- C:157-167
3	THIOL_PROTEASE_ASN	PS00640	Eukaryotic thiol (cysteine) proteases asparagine active site.	PAPA1_CARPA	303-322	1	- C:170-189

(no "Exon" information available for 3LFY)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:214
 aligned with PAPA1_CARPA | P00784 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:214
                                                                                                                                                                                                                                             345  
                                   143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343 |  
          PAPA1_CARPA   134 IPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIFVGPCGNKVDHAVAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN--   -
               SCOP domains d3lfya_ A: Papain                                                                                                                                                                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.................hhhhhhhhhhhhhhhhhhh......hhhhhhhhh...hhhhh.hhhhhhhhhhhh...............................eee....hhhhhhhhhhhh.eeeee...hhhhhh....ee.........eeeeeeee...eeeee...........eeeee.......hhhhh....eee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE--THIOL_PROTEASE_ASN  ------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lfy A   1 IPEYVDWRQKGAVTPVKNQGSCGScWAFSAVVTIEGIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIFVGPCGNKVDHAVAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKNSN 214
                                    10        20    |   30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    
                                                   25-OCS

Chain C from PDB  Type:PROTEIN  Length:215
 aligned with PAPA1_CARPA | P00784 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:215
                                                                                                                                                                                                                                             345   
                                   143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343 |   
          PAPA1_CARPA   134 IPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIFVGPCGNKVDHAVAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN---   -
               SCOP domains d3lfyc_ C: Papain                                                                                                                                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Peptidase_C1-3lfyC01 C:1-210                                                                                                                                                                                      ----- Pfam domains (1)
           Pfam domains (2) Peptidase_C1-3lfyC02 C:1-210                                                                                                                                                                                      ----- Pfam domains (2)
         Sec.struct. author ....ee.................hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhh.hhhhhhhhhh...................hhhhh........eeee....hhhhhhhhhhhh.eeeee...hhhhhhh...ee.........eeeee.ee....eeee...........eeee........hhhhh....eeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE--THIOL_PROTEASE_ASN  -------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lfy C   1 IPEYVDWRQKGAVTPVKNQGSCGScWAFSAVVTIEGIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIFVGPCGNKVDHAVAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKNSGN 215
                                    10        20    |   30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     
                                                   25-OCS

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Cysteine proteinases (392)

Superfamily: Cysteine proteinases (392)

Family: Papain-like (200)

Protein domain: Papain (22)

Papaya (Carica papaya) [TaxId: 3649] (22)

1a	d3lfya_	A:
1b	d3lfyc_	C:

(no "CATH Domain" information available for 3LFY)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_CA (169)

Family: Peptidase_C1 (81)

Carica papaya (Papaya) (14)

1a	Peptidase_C1-3lfyC01	C:1-210
1b	Peptidase_C1-3lfyC02	C:1-210

Asymmetric Unit(hide GO term definitions)

Chain A,C (PAPA1_CARPA | P00784)

molecular function
	GO:0008234	cysteine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0097655	serpin family protein binding	Interacting selectively and non-covalently with any member of the serpin protein family (serine protease inhibitors or classified inhibitor family I4). Serpins are a broadly distributed family of protease inhibitors that use a conformational change to inhibit target enzymes. They are central in controlling many important proteolytic cascades. The majority of serpins inhibit serine proteases, but serpins that inhibit caspases and papain-like cysteine proteases have also been identified. Rarely, serpins perform a non-inhibitory function; for example, several human serpins function as hormone transporters and certain serpins function as molecular chaperones or tumor suppressors.
biological process
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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	Cis Peptide Bonds
		Gly A:151 - Pro A:152	[ RasMol ]
		Gly C:151 - Pro C:152	[ RasMol ]

Biological Units
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3ima	TAROCYSTATIN IN COMPLEX WITH PAPAIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (5, 5)

SS Bonds (6, 6)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 6)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

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Pfam Domains (1, 2)

Gene Ontology (5, 5)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File